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pip install fails: "xsFortran.h: no such file or directory" #136

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JohannesBuchner opened this issue Dec 3, 2020 · 5 comments · Fixed by #137
Closed

pip install fails: "xsFortran.h: no such file or directory" #136

JohannesBuchner opened this issue Dec 3, 2020 · 5 comments · Fixed by #137

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@JohannesBuchner
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I tried to install threeML, but astromodels failed. I think it tried to use the xspec installation from my home directory -- is it looking for the source files?

This is on Ubuntu Linux 20.04, Python 3.8.5, no python environments.

$ pip install threeML
Collecting threeML
  Downloading threeML-2.0.2.tar.gz (37.3 MB)
     |████████████████████████████████| 37.3 MB 257 kB/s 
Collecting astromodels
  Downloading astromodels-2.0.1.tar.gz (855 kB)
     |████████████████████████████████| 855 kB 18.6 MB/s 
Requirement already satisfied: astropy>=1.3.3 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (4.1)
Collecting astroquery
  Using cached astroquery-0.4.1.tar.gz (6.5 MB)
Requirement already satisfied: corner in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (2.1.0)
Collecting dill
  Downloading dill-0.3.3-py2.py3-none-any.whl (81 kB)
     |████████████████████████████████| 81 kB 6.1 MB/s 
Collecting dynesty
  Using cached dynesty-1.0.1-py2.py3-none-any.whl (86 kB)
Collecting emcee>=3
  Using cached emcee-3.0.2-py2.py3-none-any.whl (41 kB)
Collecting iminuit>=1.2
  Downloading iminuit-1.5.4-cp38-cp38-manylinux2010_x86_64.whl (4.2 MB)
     |████████████████████████████████| 4.2 MB 125 kB/s 
Collecting ipyparallel
  Downloading ipyparallel-6.3.0-py3-none-any.whl (199 kB)
     |████████████████████████████████| 199 kB 17.7 MB/s 
Requirement already satisfied: ipython in /usr/lib/python3/dist-packages (from threeML) (7.13.0)
Requirement already satisfied: matplotlib in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (3.3.2)
Requirement already satisfied: numba in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (0.52.0)
Collecting numdifftools
  Downloading numdifftools-0.9.39-py2.py3-none-any.whl (953 kB)
     |████████████████████████████████| 953 kB 17.6 MB/s 
Collecting numexpr
  Downloading numexpr-2.7.1-cp38-cp38-manylinux1_x86_64.whl (164 kB)
     |████████████████████████████████| 164 kB 18.1 MB/s 
Requirement already satisfied: numpy>=1.16 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (1.19.2)
Requirement already satisfied: pandas in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (1.1.3)
Requirement already satisfied: pyyaml>=5.1 in /usr/lib/python3/dist-packages (from threeML) (5.3.1)
Requirement already satisfied: requests in /usr/lib/python3/dist-packages (from threeML) (2.22.0)
Requirement already satisfied: scipy>=0.18 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (1.5.3)
Collecting speclite<0.9
  Downloading speclite-0.8.tar.gz (599 kB)
     |████████████████████████████████| 599 kB 13.4 MB/s 
Requirement already satisfied: ultranest in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from threeML) (3.0.1)
Collecting uncertainties
  Downloading uncertainties-3.1.5-py2.py3-none-any.whl (246 kB)
     |████████████████████████████████| 246 kB 19.5 MB/s 
Requirement already satisfied: future in /usr/lib/python3/dist-packages (from astromodels->threeML) (0.18.2)
Requirement already satisfied: h5py in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from astromodels->threeML) (2.10.0)
Collecting interpolation
  Downloading interpolation-2.1.6-py3-none-any.whl (54 kB)
     |████████████████████████████████| 54 kB 627 kB/s 
Collecting tables
  Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB)
     |████████████████████████████████| 4.3 MB 27.7 MB/s 
Requirement already satisfied: beautifulsoup4>=4.3.2 in /usr/lib/python3/dist-packages (from astroquery->threeML) (4.8.2)
Requirement already satisfied: html5lib>=0.999 in /usr/lib/python3/dist-packages (from astroquery->threeML) (1.0.1)
Requirement already satisfied: keyring>=4.0 in /usr/lib/python3/dist-packages (from astroquery->threeML) (18.0.1)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from astroquery->threeML) (1.14.0)
Requirement already satisfied: setuptools>=40.6.0 in /usr/lib/python3/dist-packages (from corner->threeML) (45.2.0)
Requirement already satisfied: setuptools-scm in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from corner->threeML) (4.1.2)
Requirement already satisfied: wheel in /usr/lib/python3/dist-packages (from corner->threeML) (0.34.2)
Requirement already satisfied: tornado>=4 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from ipyparallel->threeML) (6.1)
Requirement already satisfied: pyzmq>=13 in /usr/lib/python3/dist-packages (from ipyparallel->threeML) (18.1.1)
Requirement already satisfied: jupyter-client in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from ipyparallel->threeML) (6.1.7)
Requirement already satisfied: traitlets>=4.3 in /usr/lib/python3/dist-packages (from ipyparallel->threeML) (4.3.3)
Requirement already satisfied: ipython-genutils in /usr/lib/python3/dist-packages (from ipyparallel->threeML) (0.2.0)
Requirement already satisfied: python-dateutil>=2.1 in /usr/lib/python3/dist-packages (from ipyparallel->threeML) (2.7.3)
Requirement already satisfied: ipykernel>=4.4 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from ipyparallel->threeML) (5.3.4)
Requirement already satisfied: decorator in /usr/lib/python3/dist-packages (from ipyparallel->threeML) (4.4.2)
Requirement already satisfied: pexpect in /usr/lib/python3/dist-packages (from ipython->threeML) (4.6.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /usr/lib/python3/dist-packages (from matplotlib->threeML) (2.4.6)
Requirement already satisfied: cycler>=0.10 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from matplotlib->threeML) (0.10.0)
Requirement already satisfied: pillow>=6.2.0 in /usr/lib/python3/dist-packages (from matplotlib->threeML) (7.0.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from matplotlib->threeML) (1.2.0)
Requirement already satisfied: certifi>=2020.06.20 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from matplotlib->threeML) (2020.6.20)
Requirement already satisfied: llvmlite<0.36,>=0.35.0 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from numba->threeML) (0.35.0)
Requirement already satisfied: pytz>=2017.2 in /usr/lib/python3/dist-packages (from pandas->threeML) (2019.3)
Requirement already satisfied: cython in /usr/lib/python3/dist-packages (from ultranest->threeML) (0.29.14)
Collecting tempita>=0.5.2
  Downloading Tempita-0.5.2.tar.gz (12 kB)
Requirement already satisfied: secretstorage in /usr/lib/python3/dist-packages (from keyring>=4.0->astroquery->threeML) (2.3.1)
Requirement already satisfied: jupyter-core>=4.6.0 in /mnt/data/daten/PostDoc2/home/.local/lib/python3.8/site-packages (from jupyter-client->ipyparallel->threeML) (4.7.0)
Building wheels for collected packages: threeML, astromodels, astroquery, speclite, tempita
  Building wheel for threeML (setup.py) ... done
  Created wheel for threeML: filename=threeML-2.0.2-py3-none-any.whl size=38760619 sha256=7fc6154e4893325a1d1f929a4911f6f9e3d9ccb009e68ba1783b0aeaaaf1cfa9
  Stored in directory: /mnt/data/daten/PostDoc2/home/.cache/pip/wheels/75/dc/f9/327143aea3820dcff9fe266c82b672017c7dc2641ac30f63d3
  Building wheel for astromodels (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-irk8m1vt/astromodels/setup.py'"'"'; __file__='"'"'/tmp/pip-install-irk8m1vt/astromodels/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-meub_n88
       cwd: /tmp/pip-install-irk8m1vt/astromodels/
  Complete output (124 lines):
  
   Xspec is detected. Will compile the Xspec extension.
  
  Found library XSFunctions in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
  Found library XSModel in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
  Found library XSUtil in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
  Found library XS in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
  Found library cfitsio in None
  Found library CCfits_2.5 in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
  Found library wcs-5.19.1 in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
  Found library gfortran in None
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/astromodels
  copying astromodels/__init__.py -> build/lib.linux-x86_64-3.8/astromodels
  copying astromodels/_version.py -> build/lib.linux-x86_64-3.8/astromodels
  creating build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/polarization.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/tree.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/spectral_component.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/memoization.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/thread_safe_unit_format.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/parameter_transformation.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/parameter.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/my_yaml.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/serialization.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/sky_direction.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/cpickle_compatibility_layer.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/model.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/model_parser.py -> build/lib.linux-x86_64-3.8/astromodels/core
  copying astromodels/core/units.py -> build/lib.linux-x86_64-3.8/astromodels/core
  creating build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/functions_3D.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/function.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/functions.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/numba_functions.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/priors.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/template_model.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/apec.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  copying astromodels/functions/functions_2D.py -> build/lib.linux-x86_64-3.8/astromodels/functions
  creating build/lib.linux-x86_64-3.8/astromodels/functions/dark_matter
  copying astromodels/functions/dark_matter/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/functions/dark_matter
  copying astromodels/functions/dark_matter/dm_models.py -> build/lib.linux-x86_64-3.8/astromodels/functions/dark_matter
  creating build/lib.linux-x86_64-3.8/astromodels/sources
  copying astromodels/sources/particle_source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
  copying astromodels/sources/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/sources
  copying astromodels/sources/extended_source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
  copying astromodels/sources/point_source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
  copying astromodels/sources/source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
  creating build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/pretty_list.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/valid_variable.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/angular_distance.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/table.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/disk_usage.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/long_path_formatter.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/data_files.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/configuration.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/io.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  copying astromodels/utils/vincenty.py -> build/lib.linux-x86_64-3.8/astromodels/utils
  creating build/lib.linux-x86_64-3.8/astromodels/xspec
  copying astromodels/xspec/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/xspec
  copying astromodels/xspec/factory.py -> build/lib.linux-x86_64-3.8/astromodels/xspec
  copying astromodels/xspec/xspec_settings.py -> build/lib.linux-x86_64-3.8/astromodels/xspec
  package init file 'astromodels/tests/__init__.py' not found (or not a regular file)
  creating build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_load_xspec_models.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_extended_source.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_memoizer.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_template_model.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_functions.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_parameter.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_tree.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_1D_function_values.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_model.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  copying astromodels/tests/test_point_source.py -> build/lib.linux-x86_64-3.8/astromodels/tests
  running egg_info
  writing astromodels.egg-info/PKG-INFO
  writing dependency_links to astromodels.egg-info/dependency_links.txt
  writing requirements to astromodels.egg-info/requires.txt
  writing top-level names to astromodels.egg-info/top_level.txt
  reading manifest file 'astromodels.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  writing manifest file 'astromodels.egg-info/SOURCES.txt'
  creating build/lib.linux-x86_64-3.8/astromodels/data
  creating build/lib.linux-x86_64-3.8/astromodels/data/dark_matter
  copying astromodels/data/dark_matter/dmSpecTab.npy -> build/lib.linux-x86_64-3.8/astromodels/data/dark_matter
  copying astromodels/data/dark_matter/gammamc_dif.dat -> build/lib.linux-x86_64-3.8/astromodels/data/dark_matter
  creating build/lib.linux-x86_64-3.8/astromodels/data/tests
  copying astromodels/data/tests/test_xspec_table_model.fits -> build/lib.linux-x86_64-3.8/astromodels/data/tests
  creating build/lib.linux-x86_64-3.8/astromodels/core/node_ctype
  copying astromodels/core/node_ctype/node_ctype.cxx -> build/lib.linux-x86_64-3.8/astromodels/core/node_ctype
  copying astromodels/xspec/LICENSE -> build/lib.linux-x86_64-3.8/astromodels/xspec
  copying astromodels/xspec/README -> build/lib.linux-x86_64-3.8/astromodels/xspec
  creating build/lib.linux-x86_64-3.8/astromodels/xspec/include
  creating build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
  copying astromodels/xspec/include/sherpa/array.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
  copying astromodels/xspec/include/sherpa/constants.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
  copying astromodels/xspec/include/sherpa/extension.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
  copying astromodels/xspec/include/sherpa/fcmp.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
  creating build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa/astro
  copying astromodels/xspec/include/sherpa/astro/xspec_extension.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa/astro
  creating build/lib.linux-x86_64-3.8/astromodels/xspec/src
  copying astromodels/xspec/src/_xspec.cc -> build/lib.linux-x86_64-3.8/astromodels/xspec/src
  UPDATING build/lib.linux-x86_64-3.8/astromodels/_version.py
  set build/lib.linux-x86_64-3.8/astromodels/_version.py to '2.0.1'
  running build_ext
  building 'astromodels.xspec._xspec' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/astromodels
  creating build/temp.linux-x86_64-3.8/astromodels/xspec
  creating build/temp.linux-x86_64-3.8/astromodels/xspec/src
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -I/home/user/.local/lib/python3.8/site-packages/numpy/core/include -Iastromodels/xspec/include -c astromodels/xspec/src/_xspec.cc -o build/temp.linux-x86_64-3.8/astromodels/xspec/src/_xspec.o
  astromodels/xspec/src/_xspec.cc:101:10: fatal error: xsFortran.h: No such file or directory
    101 | #include "xsFortran.h"
        |          ^~~~~~~~~~~~~
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for astromodels
  Running setup.py clean for astromodels
  Building wheel for astroquery (setup.py) ... done
  Created wheel for astroquery: filename=astroquery-0.4.1-py3-none-any.whl size=3831876 sha256=f48e2b506b8af02d717b34c32a991cb6b90105350591b373ef1631cf16f47b8d
  Stored in directory: /mnt/data/daten/PostDoc2/home/.cache/pip/wheels/38/a3/2c/65f38691eef2c25e74f1ab45186b67e09cea7b59696fd67696
  Building wheel for speclite (setup.py) ... done
  Created wheel for speclite: filename=speclite-0.8-py3-none-any.whl size=191538 sha256=c290d51b9034629decc95c74d5a59fcfb5f2a5bd07e4cacf85dc94539250fab0
  Stored in directory: /mnt/data/daten/PostDoc2/home/.cache/pip/wheels/cc/9e/50/886e16ee41f37be67bc254a5c9110567f015c35e0bf47da05b
  Building wheel for tempita (setup.py) ... done
  Created wheel for tempita: filename=Tempita-0.5.2-py3-none-any.whl size=12880 sha256=d112e3e93efe9e888b5e33320b02ec3760d9c7561f28b37884b02a22cca9d563
  Stored in directory: /mnt/data/daten/PostDoc2/home/.cache/pip/wheels/b0/b9/10/fd85fe4c1e7ed2f1864865b842a4b847a897c6246033bbd3cf
Successfully built threeML astroquery speclite tempita
Failed to build astromodels
Installing collected packages: dill, tempita, interpolation, numexpr, tables, astromodels, astroquery, dynesty, emcee, iminuit, ipyparallel, numdifftools, speclite, uncertainties, threeML
    Running setup.py install for astromodels ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-irk8m1vt/astromodels/setup.py'"'"'; __file__='"'"'/tmp/pip-install-irk8m1vt/astromodels/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-qy8cl6zy/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/user/.local/include/python3.8/astromodels
         cwd: /tmp/pip-install-irk8m1vt/astromodels/
    Complete output (124 lines):
    
     Xspec is detected. Will compile the Xspec extension.
    
    Found library XSFunctions in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
    Found library XSModel in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
    Found library XSUtil in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
    Found library XS in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
    Found library cfitsio in None
    Found library CCfits_2.5 in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
    Found library wcs-5.19.1 in /home/user/bin/xspec-6.28/x86_64-pc-linux-gnu-libc2.31/lib
    Found library gfortran in None
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.8
    creating build/lib.linux-x86_64-3.8/astromodels
    copying astromodels/__init__.py -> build/lib.linux-x86_64-3.8/astromodels
    copying astromodels/_version.py -> build/lib.linux-x86_64-3.8/astromodels
    creating build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/polarization.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/tree.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/spectral_component.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/memoization.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/thread_safe_unit_format.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/parameter_transformation.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/parameter.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/my_yaml.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/serialization.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/sky_direction.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/cpickle_compatibility_layer.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/model.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/model_parser.py -> build/lib.linux-x86_64-3.8/astromodels/core
    copying astromodels/core/units.py -> build/lib.linux-x86_64-3.8/astromodels/core
    creating build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/functions_3D.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/function.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/functions.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/numba_functions.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/priors.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/template_model.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/apec.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    copying astromodels/functions/functions_2D.py -> build/lib.linux-x86_64-3.8/astromodels/functions
    creating build/lib.linux-x86_64-3.8/astromodels/functions/dark_matter
    copying astromodels/functions/dark_matter/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/functions/dark_matter
    copying astromodels/functions/dark_matter/dm_models.py -> build/lib.linux-x86_64-3.8/astromodels/functions/dark_matter
    creating build/lib.linux-x86_64-3.8/astromodels/sources
    copying astromodels/sources/particle_source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
    copying astromodels/sources/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/sources
    copying astromodels/sources/extended_source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
    copying astromodels/sources/point_source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
    copying astromodels/sources/source.py -> build/lib.linux-x86_64-3.8/astromodels/sources
    creating build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/pretty_list.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/valid_variable.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/angular_distance.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/table.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/disk_usage.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/long_path_formatter.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/data_files.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/configuration.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/io.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    copying astromodels/utils/vincenty.py -> build/lib.linux-x86_64-3.8/astromodels/utils
    creating build/lib.linux-x86_64-3.8/astromodels/xspec
    copying astromodels/xspec/__init__.py -> build/lib.linux-x86_64-3.8/astromodels/xspec
    copying astromodels/xspec/factory.py -> build/lib.linux-x86_64-3.8/astromodels/xspec
    copying astromodels/xspec/xspec_settings.py -> build/lib.linux-x86_64-3.8/astromodels/xspec
    package init file 'astromodels/tests/__init__.py' not found (or not a regular file)
    creating build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_load_xspec_models.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_extended_source.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_memoizer.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_template_model.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_functions.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_parameter.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_tree.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_1D_function_values.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_model.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    copying astromodels/tests/test_point_source.py -> build/lib.linux-x86_64-3.8/astromodels/tests
    running egg_info
    writing astromodels.egg-info/PKG-INFO
    writing dependency_links to astromodels.egg-info/dependency_links.txt
    writing requirements to astromodels.egg-info/requires.txt
    writing top-level names to astromodels.egg-info/top_level.txt
    reading manifest file 'astromodels.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'astromodels.egg-info/SOURCES.txt'
    creating build/lib.linux-x86_64-3.8/astromodels/data
    creating build/lib.linux-x86_64-3.8/astromodels/data/dark_matter
    copying astromodels/data/dark_matter/dmSpecTab.npy -> build/lib.linux-x86_64-3.8/astromodels/data/dark_matter
    copying astromodels/data/dark_matter/gammamc_dif.dat -> build/lib.linux-x86_64-3.8/astromodels/data/dark_matter
    creating build/lib.linux-x86_64-3.8/astromodels/data/tests
    copying astromodels/data/tests/test_xspec_table_model.fits -> build/lib.linux-x86_64-3.8/astromodels/data/tests
    creating build/lib.linux-x86_64-3.8/astromodels/core/node_ctype
    copying astromodels/core/node_ctype/node_ctype.cxx -> build/lib.linux-x86_64-3.8/astromodels/core/node_ctype
    copying astromodels/xspec/LICENSE -> build/lib.linux-x86_64-3.8/astromodels/xspec
    copying astromodels/xspec/README -> build/lib.linux-x86_64-3.8/astromodels/xspec
    creating build/lib.linux-x86_64-3.8/astromodels/xspec/include
    creating build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
    copying astromodels/xspec/include/sherpa/array.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
    copying astromodels/xspec/include/sherpa/constants.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
    copying astromodels/xspec/include/sherpa/extension.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
    copying astromodels/xspec/include/sherpa/fcmp.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa
    creating build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa/astro
    copying astromodels/xspec/include/sherpa/astro/xspec_extension.hh -> build/lib.linux-x86_64-3.8/astromodels/xspec/include/sherpa/astro
    creating build/lib.linux-x86_64-3.8/astromodels/xspec/src
    copying astromodels/xspec/src/_xspec.cc -> build/lib.linux-x86_64-3.8/astromodels/xspec/src
    UPDATING build/lib.linux-x86_64-3.8/astromodels/_version.py
    set build/lib.linux-x86_64-3.8/astromodels/_version.py to '2.0.1'
    running build_ext
    building 'astromodels.xspec._xspec' extension
    creating build/temp.linux-x86_64-3.8
    creating build/temp.linux-x86_64-3.8/astromodels
    creating build/temp.linux-x86_64-3.8/astromodels/xspec
    creating build/temp.linux-x86_64-3.8/astromodels/xspec/src
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -I/home/user/.local/lib/python3.8/site-packages/numpy/core/include -Iastromodels/xspec/include -c astromodels/xspec/src/_xspec.cc -o build/temp.linux-x86_64-3.8/astromodels/xspec/src/_xspec.o
    astromodels/xspec/src/_xspec.cc:101:10: fatal error: xsFortran.h: No such file or directory
      101 | #include "xsFortran.h"
          |          ^~~~~~~~~~~~~
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-irk8m1vt/astromodels/setup.py'"'"'; __file__='"'"'/tmp/pip-install-irk8m1vt/astromodels/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-qy8cl6zy/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/user/.local/include/python3.8/astromodels Check the logs for full command output.
@grburgess
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It will detected if the HEADAS environment variable is set and then tries to load the library with ctypes. I think we need to print out more debug info when this fails and escape the failure.

Temporary solutions:

  • unset HEADAS and it will install without XSPEC
  • the conda install will automatically include XSPEC

you can also clone and try to print out some info from he setup file looking here:

https://github.com/threeML/astromodels/blob/master/setup.py#L56

and here:

https://github.com/threeML/astromodels/blob/master/setup.py#L228

@ndilalla We (?) need to write some more info for the XSPEC install.. it may be outdated, but I think we do not cover all the corner cases.

@JohannesBuchner
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build_ext does not sound like ctypes, more like it is trying to compile astromodels/xspec/src/_xspec.cc against xspec headers.

@grburgess
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I think the issue is that it finds the libs, but we currently assume the headers are in a normal place. I'm cooking up a solution now.

@grburgess
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@JohannesBuchner Ok, I believe the issues is fixed in #137
If you checkout this branch (xspec_setup) and install manually, it should go smoothly.

@ndilalla can we speed release this one as it can easily break pip install?

@ndilalla ndilalla linked a pull request Dec 3, 2020 that will close this issue
Xspec setup #137
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@parsotat parsotat mentioned this issue Sep 22, 2023
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@parsotat
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I have run into this issue again and the suggestion in the error message did not work for me for setting XSPEC_INC_PATH (see grburgess/ronswanson#11). what I had to do was env -u HEADAS pip install ronswanson and the package seemed to install correctly without the Xspec compatibility. I would like to be able to have that compatibility so any suggestions would be helpful

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Xspec setup threeML/astromodels
3 participants
@JohannesBuchner @grburgess @parsotat